Yoga 2 11 Windows closes all my programs when I close the lid

Lenovo Yoga 2 11
Model 20332
Windows 8.1 64-bit
When I close the lid of the tablet/laptop, I expect that Windows will go to sleep and that when I open the computer and login, all of my windows and programs should be open as I had them when I closed the lid. Sometimes, this is the case. But other times, when I open the lid, it's as if I had logged completely out -- no windows are open, and any programs running in the notification area (e.g. Bittorrent Sync) are no longer running.
How do I configure this so that my programs are not closed when I close the lid or otherwise make the computer go to sleep?
My current Windows settings:
Control Panel > Power Options: Daily Plan
Turn off the display: On battery: 10 minutes, Plugged in: 30 minutes
Put the computer to sleep: On battery: 30 minutes, Plugged in: 1 hour
Allow hybrid sleep: On battery: On, Plugged in: On
Hibernate after: On battery: 120 Minutes, Plugged in: Never
Power and sleep buttons and lid settings:
When I press the power button: On battery: Hibernate, Plugged in: Sleep
When I press the sleep button: On battery: Sleep, Plugged in: Sleep
When I close the lid: On battery: Sleep, Plugged in: Sleep

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Yoga 2 11 Windows closes all my programs when I close the lid

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